Platanus-allee phasing fail: Error(13): Error, SolveDBG exception!!
1
2
Entering edit mode
4.7 years ago

Hello there,

I am using Platanus-allee 2.2.2 to generate hybrid assembly of Illumina short reads and PacBio reads. I have got contigs.fa from short reads but phasing step with PacBio reads gives the following error after running for couple of hours

Error(13): Error, SolveDBG exception!! platanus_allee solve_DBG command failed.

Here is the script used for contig assembly and phasing

num_threads=20 
tmp_dir=/path-to-/tem/platanus_allee 
memory_GB=100 
out_prefix=out
minimap2_path=minimap2

# Input reads

PE=trimmed_L1_*.fq
PacBio=pacbio*.fastq.gz

# Contig assembly commands
platanus_allee assemble -t ${num_threads} -tmp ${tmp_dir} -m ${memory_GB} -o ${out_prefix} \
-f $PE \
2>${out_prefix}.assembleLog

# phasing commands 
platanus_allee phase -t ${num_threads} -tmp ${tmp_dir} -o ${out_prefix} -mapper ${minimap2_path} \
-c out_contig.fa \
-IP1 $PE -p $PacBio \ 
2>${out_prefix}.phaseLog

cat out.phaseLog

platanus_allee version: 2.2.2
platanus_allee phase -t 20 -tmp /path-to-/tem/platanus_allee -o out -mapper minimap2 -c out_contig.fa -IP1 trimmed_L1_1.fq trimmed_L1_2.fq -p /path-to-/pacbio*.fastq.gz 

Error(13): Error, SolveDBG exception!!
platanus_allee solve_DBG command failed. 

tail -n 15 path-to-/out_intermediateResults/round1/out.solveDBGLog

dividing nodes based on bubbles ...
dividing scaffolds to adjust bubble-breakpoints...
dividing indonsistent bubble-ends...
pairing bubble nodes...
dividing scaffolds to adjust bubble-breakpoints distiguishing strands ...
NUM_DIVISION = 1832
dividing scaffolds to adjust bubble-breakpoints...
dividing indonsistent bubble-ends...
pairing bubble nodes...
dividing scaffolds to adjust bubble-breakpoints distiguishing strands ...
NUM_DIVISION = 0
TOTAL_NUM_DIVISIONS =1832

dividing erroneous scaffolds based on base-level coverages ...
Segmentation fault (core dumped)

A bug causing the segmentation fault seems issue on Platanus-allee v2.0.0 and earlier

Any suggestion please?

genome next-gen software-error Assembly • 2.4k views
ADD COMMENT
0
Entering edit mode

I'm running into the same issue - platanus_allee assemble worked, but I get the error code when running the phasing command.

Did you end up finding a solution?

ADD REPLY
0
Entering edit mode

Hi, I did not find a way to work it out and finally gave up on it and switched to my focus to SPAdes.

ADD REPLY
0
Entering edit mode

Hello, I am also getting the same error using the 2.2.2 version. Also wrote to the authors but no answer. Did anybody found a solution? The original paper has been cited 25 times (according to WOS) so I assume this error is not a bug?

ADD REPLY

Login before adding your answer.

Traffic: 2146 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6